assembly_id	genome_id	genome_def	crispr_array_locus_merge	crispr_array_location_merge	crispr_locus_id	crispr_pred_method	array_in_prot	prot_within_array_20000	prot_in_genome	crispr_type_by_cas_prot	consensus_repeat	repeat_length	self-targeting_spacer_number	self-targeting_target_number	spacer_location	protospacer_location	repeat_type	spacer_locus_num	spacer_num	correct_crispr_type	genome_cas_prots	unknown_protein_around_crispr	L10	L10_domain	L9	L9_domain	L8	L8_domain	L7	L7_domain	L6	L6_domain	L5	L5_domain	L4	L4_domain	L3	L3_domain	L2	L2_domain	L1	L1_domain	R1	R1_domain	R2	R2_domain	R3	R3_domain	R4	R4_domain	R5	R5_domain	R6	R6_domain	R7	R7_domain	R8	R8_domain	R9	R9_domain	R10	R10_domain
GCF_001483405.1_ASM148340v1	NZ_CP013722	Listeria monocytogenes strain Lm 3163 chromosome, complete genome	1	976133-979019	1,1,1	CRISPRCasFinder,CRT,PILER-CR	no	cas2,cas1,cas4,cas3,cas5,cas7,cas8b2,cas6	cas3,DEDDh,cas2,cas1,cas4,cas5,cas7,cas8b2,cas6,casR,WYL,DinG,csa3,cas9,csn2	Unclear	ATTTACATTTCATAATAAGTAGTTAAAAC,ATTTACATTTCATAATAAGTAGTTAAAAC,ATTTACATTTCATAATAAGTAGTTAAAAC	29,29,29	2	2	976812-976847|977073-977106	NZ_CP013722.1_1946902-1946867|NZ_CP013722.1_983181-983148	I-A:I-A:I-A	44,44,43	44	Unclear	cas3,DEDDh,cas2,cas1,cas4,cas5,cas7,cas8b2,cas6,casR,WYL,DinG,csa3,cas9,csn2	NA|488aa|up_9|NZ_CP013722.1_964368_965832_-,NA|148aa|up_5|NZ_CP013722.1_970141_970585_-,NA	NA|488aa|up_9|NZ_CP013722.1_964368_965832_-	NA	NA|247aa|up_8|NZ_CP013722.1_966061_966802_+	cd01106, HTH_TipAL-Mta, Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA	NA|444aa|up_7|NZ_CP013722.1_966847_968179_-	COG5361, COG5361, Uncharacterized conserved protein [Function unknown]	NA|554aa|up_6|NZ_CP013722.1_968434_970096_+	COG0659, SUL1, Sulfate permease and related transporters (MFS superfamily) [Inorganic ion transport and metabolism]	NA|148aa|up_5|NZ_CP013722.1_970141_970585_-	NA	NA|251aa|up_4|NZ_CP013722.1_970690_971443_-	COG1737, RpiR, Transcriptional regulators [Transcription]	NA|439aa|up_3|NZ_CP013722.1_971645_972962_+	cd05296, GH4_P_beta_glucosidase, Glycoside Hydrolases Family 4; Phospho-beta-glucosidase	NA|335aa|up_2|NZ_CP013722.1_972993_973998_-	COG1940, NagC, Transcriptional regulator/sugar kinase [Transcription / Carbohydrate transport and metabolism]	NA|472aa|up_1|NZ_CP013722.1_974129_975545_-	TIGR00711, Uncharacterized_MFS-type_transporter_YhcA, drug resistance transporter, EmrB/QacA subfamily	NA|123aa|up_0|NZ_CP013722.1_975692_976061_+	COG3759, COG3759, Predicted membrane protein [Function unknown]	cas2|93aa|down_0|NZ_CP013722.1_979216_979495_-	cd09725, Cas2_I_II_III, CRISPR/Cas system-associated protein Cas2	cas1|330aa|down_1|NZ_CP013722.1_979499_980489_-	TIGR03641, cas1_HMARI, CRISPR-associated endonuclease Cas1, subtype I-B/HMARI/TNEAP	cas4|163aa|down_2|NZ_CP013722.1_980501_980990_-	pfam01930, Cas_Cas4, Domain of unknown function DUF83	cas3|736aa|down_3|NZ_CP013722.1_981003_983211_-	COG1203, COG1203, CRISPR-associated helicase Cas3 [Defense mechanisms]	cas5|261aa|down_4|NZ_CP013722.1_983278_984061_-	TIGR01895, conserved_hypothetical_protein, CRISPR-associated protein Cas5, subtype I-B/TNEAP	cas7|290aa|down_5|NZ_CP013722.1_984038_984908_-	TIGR02585, conserved_protein, CRISPR-associated protein Cas7/Cst2/DevR, subtype I-B/TNEAP	cas8b2|563aa|down_6|NZ_CP013722.1_984897_986586_-	cd09754, Cas8a1_I-A, CRISPR/Cas system-associated protein Cas8a1	cas6|241aa|down_7|NZ_CP013722.1_986601_987324_-	TIGR01877, CRISPR-associated_endoribonuclease_Cas6_1, CRISPR-associated endoribonuclease Cas6	NA|272aa|down_8|NZ_CP013722.1_987676_988492_+	COG0406, phoE, Broad specificity phosphatase PhoE and related phosphatases [General function prediction only]	NA|477aa|down_9|NZ_CP013722.1_988612_990043_+	COG2843, PgsA, Putative enzyme of poly-gamma-glutamate biosynthesis (capsule formation) [Cell envelope biogenesis, outer membrane]
GCF_001483405.1_ASM148340v1	NZ_CP013722	Listeria monocytogenes strain Lm 3163 chromosome, complete genome	2	996714-997191	2,2,2	PILER-CR,CRISPRCasFinder,CRT	no	cas2,cas1,cas4,cas3,cas5,cas7,cas8b2,cas6	cas3,DEDDh,cas2,cas1,cas4,cas5,cas7,cas8b2,cas6,casR,WYL,DinG,csa3,cas9,csn2	Unclear	ATTTACATTTCACAATAAGTAACTAAAA,ATTTACATTTCACAATAAGTAACTAAAA,ATTTACATTTCACAATAAGTAACTAAAAC	28,28,29	1	1	996743-996777	NZ_CP013722.1_1970471-1970505	I-A:I-A:I-A	7,7,7	7	Unclear	cas3,DEDDh,cas2,cas1,cas4,cas5,cas7,cas8b2,cas6,casR,WYL,DinG,csa3,cas9,csn2	NA|193aa|up_0|NZ_CP013722.1_995743_996322_-,NA|133aa|down_5|NZ_CP013722.1_1001802_1002201_-	cas6|241aa|up_9|NZ_CP013722.1_986601_987324_-	TIGR01877, CRISPR-associated_endoribonuclease_Cas6_1, CRISPR-associated endoribonuclease Cas6	NA|272aa|up_8|NZ_CP013722.1_987676_988492_+	COG0406, phoE, Broad specificity phosphatase PhoE and related phosphatases [General function prediction only]	NA|477aa|up_7|NZ_CP013722.1_988612_990043_+	COG2843, PgsA, Putative enzyme of poly-gamma-glutamate biosynthesis (capsule formation) [Cell envelope biogenesis, outer membrane]	NA|144aa|up_6|NZ_CP013722.1_990089_990521_-	pfam00582, Usp, Universal stress protein family	NA|612aa|up_5|NZ_CP013722.1_990621_992457_-	NF033186, internalin_K, class 1 internalin InlK	NA|153aa|up_4|NZ_CP013722.1_992838_993297_+	pfam12802, MarR_2, MarR family	NA|120aa|up_3|NZ_CP013722.1_993303_993663_+	TIGR02058, lin0512_fam, conserved hypothetical protein	NA|380aa|up_2|NZ_CP013722.1_993727_994866_-	PHA02517, PHA02517, putative transposase OrfB; Reviewed	NA|227aa|up_1|NZ_CP013722.1_994955_995636_-	cd01741, GATase1_1, Subgroup of proteins having the Type 1 glutamine amidotransferase (GATase1) domain	NA|193aa|up_0|NZ_CP013722.1_995743_996322_-	NA	NA|312aa|down_0|NZ_CP013722.1_997428_998364_-	PRK01259, PRK01259, ribose-phosphate diphosphokinase	NA|424aa|down_1|NZ_CP013722.1_998503_999775_-	COG3775, GatC, Phosphotransferase system, galactitol-specific IIC component [Carbohydrate transport and metabolism]	NA|98aa|down_2|NZ_CP013722.1_999789_1000083_-	cd05566, PTS_IIB_galactitol, PTS_IIB_galactitol: subunit IIB of enzyme II (EII) of the galactitol-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS)	NA|349aa|down_3|NZ_CP013722.1_1000098_1001145_-	cd08236, sugar_DH, NAD(P)-dependent sugar dehydrogenases	NA|217aa|down_4|NZ_CP013722.1_1001141_1001792_-	COG0036, Rpe, Pentose-5-phosphate-3-epimerase [Carbohydrate transport and metabolism]	NA|133aa|down_5|NZ_CP013722.1_1001802_1002201_-	NA	NA|156aa|down_6|NZ_CP013722.1_1002217_1002685_-	cd00211, PTS_IIA_fru, PTS_IIA, PTS system, fructose/mannitol specific IIA subunit	NA|201aa|down_7|NZ_CP013722.1_1002712_1003315_-	COG0794, GutQ, Predicted sugar phosphate isomerase involved in capsule formation [Cell envelope biogenesis, outer membrane]	NA|687aa|down_8|NZ_CP013722.1_1003318_1005379_-	COG3711, BglG, Transcriptional antiterminator [Transcription]	NA|217aa|down_9|NZ_CP013722.1_1005487_1006138_-	COG0176, MipB, Transaldolase [Carbohydrate transport and metabolism]
GCF_001483405.1_ASM148340v1	NZ_CP013722	Listeria monocytogenes strain Lm 3163 chromosome, complete genome	3	1317259-1317410	3	CRISPRCasFinder	no	cas3	cas3,DEDDh,cas2,cas1,cas4,cas5,cas7,cas8b2,cas6,casR,WYL,DinG,csa3,cas9,csn2	Unclear	GAGCTCGGTTCCGATGTAGCAGGAGCATTAAAACCAAGAAGCATTGG	47	0	0	NA	NA	NA	1	1	Unclear	cas3,DEDDh,cas2,cas1,cas4,cas5,cas7,cas8b2,cas6,casR,WYL,DinG,csa3,cas9,csn2	NA,NA	cas3|1180aa|up_9|NZ_CP013722.1_1306383_1309923_-	COG1197, Mfd, Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]	NA|187aa|up_8|NZ_CP013722.1_1310037_1310598_-	PRK05426, PRK05426, peptidyl-tRNA hydrolase; Provisional	NA|195aa|up_7|NZ_CP013722.1_1310704_1311289_-	pfam13508, Acetyltransf_7, Acetyltransferase (GNAT) domain	NA|208aa|up_6|NZ_CP013722.1_1311378_1312002_-	PRK05618, PRK05618, 50S ribosomal protein L25/general stress protein Ctc; Reviewed	NA|314aa|up_5|NZ_CP013722.1_1312295_1313237_+	PRK00066, ldh, L-lactate dehydrogenase; Reviewed	NA|225aa|up_4|NZ_CP013722.1_1313313_1313988_+	pfam08713, DNA_alkylation, DNA alkylation repair enzyme	NA|111aa|up_3|NZ_CP013722.1_1314054_1314387_+	PRK01119, PRK01119, putative heavy metal-binding protein	NA|154aa|up_2|NZ_CP013722.1_1314437_1314899_-	COG4808, COG4808, Uncharacterized protein conserved in bacteria [Function unknown]	NA|108aa|up_1|NZ_CP013722.1_1315033_1315357_-	pfam17606, DUF5502, Family of unknown function (DUF5502)	NA|290aa|up_0|NZ_CP013722.1_1315428_1316298_-	smart00770, Zn_dep_PLPC, Zinc dependent phospholipase C (alpha toxin)	NA|511aa|down_0|NZ_CP013722.1_1318451_1319984_-	COG3227, LasB, Zinc metalloprotease (elastase) [Amino acid transport and metabolism]	NA|530aa|down_1|NZ_CP013722.1_1320314_1321904_-	pfam01289, Thiol_cytolysin, Thiol-activated cytolysin	NA|318aa|down_2|NZ_CP013722.1_1322145_1323099_+	cd00137, PI-PLCc, Catalytic domain of prokaryotic and eukaryotic phosphoinositide-specific phospholipase C	NA|238aa|down_3|NZ_CP013722.1_1323369_1324083_+	COG0664, Crp, cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]	NA|319aa|down_4|NZ_CP013722.1_1324125_1325082_-	PRK01259, PRK01259, ribose-phosphate diphosphokinase	NA|458aa|down_5|NZ_CP013722.1_1325132_1326506_-	PRK14354, glmU, bifunctional UDP-N-acetylglucosamine diphosphorylase/glucosamine-1-phosphate N-acetyltransferase GlmU	NA|103aa|down_6|NZ_CP013722.1_1326892_1327201_-	PRK13259, PRK13259, septation regulator SpoVG	NA|103aa|down_7|NZ_CP013722.1_1327320_1327629_-	PRK13259, PRK13259, septation regulator SpoVG	NA|403aa|down_8|NZ_CP013722.1_1328313_1329522_-	PRK10535, PRK10535, macrolide ABC transporter ATP-binding protein/permease MacB	NA|231aa|down_9|NZ_CP013722.1_1329518_1330211_-	cd03255, ABC_MJ0796_LolCDE_FtsE, ATP-binding cassette domain of the transporters involved in export of lipoprotein and macrolide, and cell division protein
GCF_001483405.1_ASM148340v1	NZ_CP013722	Listeria monocytogenes strain Lm 3163 chromosome, complete genome	4	1793158-1794580	4,3,3	CRISPRCasFinder,CRT,PILER-CR	no	cas9,cas1,cas2,csn2	cas3,DEDDh,cas2,cas1,cas4,cas5,cas7,cas8b2,cas6,casR,WYL,DinG,csa3,cas9,csn2	Type II-C,Type II-B,Type II-A	GTTTTAGAGCTATGTTATTTTGAATGCTACCAAAAC,GTTTTAGAGCTATGTTATTTTGAATGCTACCAAAAC,GTTTTAGAGCTATGTTATTTTGAATGCTACCAAAAC	36,36,36	0	0	NA	NA	II-A,II-B:II-A,II-B:II-A,II-B	21,21,7	21	TypeII-C,TypeII-B,TypeII-A	cas3,DEDDh,cas2,cas1,cas4,cas5,cas7,cas8b2,cas6,casR,WYL,DinG,csa3,cas9,csn2	NA|160aa|up_4|NZ_CP013722.1_1786178_1786658_+,NA|120aa|down_0|NZ_CP013722.1_1795121_1795481_+	NA|289aa|up_9|NZ_CP013722.1_1782529_1783396_+	PRK13634, cbiO, cobalt transporter ATP-binding subunit; Provisional	NA|266aa|up_8|NZ_CP013722.1_1783398_1784196_+	COG0619, CbiQ, ABC-type cobalt transport system, permease component CbiQ and related transporters [Inorganic ion transport and metabolism]	NA|249aa|up_7|NZ_CP013722.1_1784201_1784948_+	PRK00021, truA, tRNA pseudouridine(38-40) synthase TruA	NA|146aa|up_6|NZ_CP013722.1_1785142_1785580_+	PRK09216, rplM, 50S ribosomal protein L13; Reviewed	NA|131aa|up_5|NZ_CP013722.1_1785601_1785994_+	PRK00132, rpsI, 30S ribosomal protein S9; Reviewed	NA|160aa|up_4|NZ_CP013722.1_1786178_1786658_+	NA	cas9|1335aa|up_3|NZ_CP013722.1_1787167_1791172_+	COG3513, COG3513, Predicted CRISPR-associated nuclease, contains McrA/HNH-nuclease and RuvC-like nuclease domain [Defense mechanisms]	cas1|289aa|up_2|NZ_CP013722.1_1791172_1792039_+	cd09720, Cas1_II, CRISPR/Cas system-associated protein Cas1	cas2|114aa|up_1|NZ_CP013722.1_1792035_1792377_+	COG3512, COG3512, CRISPR-associated protein, Cas2 homolog [Defense mechanisms]	csn2|221aa|up_0|NZ_CP013722.1_1792366_1793029_+	cd09758, Csn2, CRISPR/Cas system-associated protein Csn2	NA|120aa|down_0|NZ_CP013722.1_1795121_1795481_+	NA	NA|141aa|down_1|NZ_CP013722.1_1795603_1796026_+	cd01109, HTH_YyaN, Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB	NA|284aa|down_2|NZ_CP013722.1_1796047_1796899_+	cd19133, AKR_AKR5F1, the AKR5F family of aldo-keto reductase (AKR)	NA|509aa|down_3|NZ_CP013722.1_1796940_1798467_-	COG1705, FlgJ, Muramidase (flagellum-specific) [Cell motility and secretion / Intracellular trafficking and secretion]	NA|343aa|down_4|NZ_CP013722.1_1798735_1799764_+	pfam10609, ParA, NUBPL iron-transfer P-loop NTPase	NA|296aa|down_5|NZ_CP013722.1_1805555_1806443_+	COG1309, AcrR, Transcriptional regulator [Transcription]	NA|494aa|down_6|NZ_CP013722.1_1806543_1808025_+	TIGR00711, Uncharacterized_MFS-type_transporter_YhcA, drug resistance transporter, EmrB/QacA subfamily	NA|281aa|down_7|NZ_CP013722.1_1808072_1808915_-	COG1912, COG1912, Uncharacterized conserved protein [Function unknown]	NA|996aa|down_8|NZ_CP013722.1_1809413_1812401_+	COG3383, COG3383, Uncharacterized anaerobic dehydrogenase [General function prediction only]	NA|159aa|down_9|NZ_CP013722.1_1812400_1812877_+	COG2427, COG2427, Uncharacterized conserved protein [Function unknown]
GCF_001483405.1_ASM148340v1	NZ_CP013722	Listeria monocytogenes strain Lm 3163 chromosome, complete genome	5	1933077-1933233	5	CRISPRCasFinder	no		cas3,DEDDh,cas2,cas1,cas4,cas5,cas7,cas8b2,cas6,casR,WYL,DinG,csa3,cas9,csn2	Orphan	ATTTAGGTAAATTTTGAAAATCAGG	25	0	0	NA	NA	NA	2	2	Orphan	cas3,DEDDh,cas2,cas1,cas4,cas5,cas7,cas8b2,cas6,casR,WYL,DinG,csa3,cas9,csn2	NA,NA|170aa|down_4|NZ_CP013722.1_1939118_1939628_-,NA|79aa|down_8|NZ_CP013722.1_1940889_1941126_+,NA|118aa|down_9|NZ_CP013722.1_1941122_1941476_+	NA|166aa|up_9|NZ_CP013722.1_1921560_1922058_+	cd04647, LbH_MAT_like, Maltose O-acyltransferase (MAT)-like: This family is composed of maltose O-acetyltransferase, galactoside O-acetyltransferase (GAT), xenobiotic acyltransferase (XAT) and similar proteins	NA|492aa|up_8|NZ_CP013722.1_1922143_1923619_+	sd00006, TPR, Tetratricopeptide repeat	NA|320aa|up_7|NZ_CP013722.1_1923697_1924657_+	TIGR01292, Thioredoxin_reductase, thioredoxin-disulfide reductase	NA|328aa|up_6|NZ_CP013722.1_1924775_1925759_+	COG1087, GalE, UDP-glucose 4-epimerase [Cell envelope biogenesis, outer membrane]	NA|354aa|up_5|NZ_CP013722.1_1925775_1926837_+	cd09019, galactose_mutarotase_like, galactose mutarotase_like	NA|577aa|up_4|NZ_CP013722.1_1926878_1928609_+	cd05799, PGM2, This CD includes PGM2 (phosphoglucomutase 2) and PGM2L1 (phosphoglucomutase 2-like 1)	NA|292aa|up_3|NZ_CP013722.1_1928716_1929592_+	PRK05416, PRK05416, RNase adapter RapZ	NA|323aa|up_2|NZ_CP013722.1_1929593_1930562_+	TIGR01826, Putative_gluconeogenesis_factor, conserved hypothetical protein, cofD-related	NA|324aa|up_1|NZ_CP013722.1_1930569_1931541_+	COG1481, COG1481, Uncharacterized protein conserved in bacteria [Function unknown]	NA|339aa|up_0|NZ_CP013722.1_1931567_1932584_+	PRK13523, PRK13523, NADPH dehydrogenase NamA; Provisional	NA|464aa|down_0|NZ_CP013722.1_1934020_1935412_+	TIGR00909, putative_amino_acid_transporter, amino acid transporter	NA|199aa|down_1|NZ_CP013722.1_1935459_1936056_-	PRK00277, clpP, ATP-dependent Clp protease proteolytic subunit; Reviewed	NA|479aa|down_2|NZ_CP013722.1_1936212_1937649_+	COG3397, COG3397, Uncharacterized protein conserved in bacteria [Function unknown]	NA|377aa|down_3|NZ_CP013722.1_1937924_1939055_-	cd01189, INT_ICEBs1_C_like, C-terminal catalytic domain of integrases from bacterial phages and conjugate transposons	NA|170aa|down_4|NZ_CP013722.1_1939118_1939628_-	NA	NA|164aa|down_5|NZ_CP013722.1_1939654_1940146_-	pfam06114, Peptidase_M78, IrrE N-terminal-like domain	NA|103aa|down_6|NZ_CP013722.1_1940177_1940486_-	cd00093, HTH_XRE, Helix-turn-helix XRE-family like proteins	NA|84aa|down_7|NZ_CP013722.1_1940634_1940886_+	cd00093, HTH_XRE, Helix-turn-helix XRE-family like proteins	NA|79aa|down_8|NZ_CP013722.1_1940889_1941126_+	NA	NA|118aa|down_9|NZ_CP013722.1_1941122_1941476_+	NA
